Open colindaven opened 8 years ago
Solution:
The above set was created using an index.
~/NAS01/programs/minimap/minimap -d backbone_raw_cln.mmi backbone_raw_cln.fasta
~/NAS01/programs/minimap/minimap backbone_raw_cln.mmi -t 50 pacbio.fa > overlaps2.paf
When not using an indexed fasta, the expected better results were created which include the reference contig name.
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/108989/0_7665 7665 179 361 + Backbone_15031 103774 86374 86540 97 182 255 cm:i:12
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/108991/2366_8564 6198 1247 5478 + Backbone_32890 17695 7564 11932 232 4368 255 cm:i:20
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/108991/2366_8564 6198 1076 6172 - Backbone_32890 17695 7968 12792 197 5096 255 cm:i:14
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/108991/2366_8564 6198 1065 3152 + Backbone_27781 25911 21331 23112 83 2087 255 cm:i:7
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/108991/2366_8564 6198 1663 3161 - Backbone_5738 111594 714 2729 65 2015 255 cm:i:6
Do you have a small test data set with which I can reproduce the issue? Thanks.
I sent a msg to your personal email @me.com
===== Mini test case for bug =====
Note - I could not reproduce the original bug with this small test case - sorry. However these other problems cropped up with the index.mmi.
tar -xvf index_test.tgz
~/NAS01/programs/minimap/minimap -d index.mmi ref.fasta ~/NAS01/programs/minimap/minimap -d index.mmi ref_align_error.fasta ~/NAS01/programs/minimap/minimap -d index.mmi ref_segfault.fasta ~/NAS01/programs/minimap/minimap -d index.mmi ref_big.fasta
~/NAS01/programs/minimap/minimap index.mmi -t 1 reads.fa > ovl.paf
Segmentation fault (core dumped)
minimap: sketch.c:59: mm_sketch: Assertion `len > 0 && w > 0 && k > 0' failed. Aborted (core dumped)
~/NAS01/programs/minimap/minimap ref.fasta -t 1 reads.fa > ovl.paf
Hi,
minimap version - downloaded from github today, so latest commit.
I have a fasta with sequence names like this:
My result.paf looks like this, minimap completes without an error. It seems the Target sequence name string is not being written. Are the names in the input fasta inappropriate ? How should the fastaheaders look ?